Difference between revisions of "Benchmarking & Scaling Tutorial/Manual Benchmarking"
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=== Prepare your input === | === Prepare your input === | ||
| − | + | It is always a good idea to create some test input for your simulation. If you have a specific system you want to benchmark for a production run make sure you limit the time the simulation is run for. If you also want to test some code given different input sizes of data, prepare those systems (or data-sets) beforehand. | |
For this tutorials purpose we are using the Molecular Dynamics Code [https://manual.gromacs.org/documentation/ GROMACS] as this is a common simulation program and readily available on most clusters. We prepared three test systems with increasing amounts of water molecules which you can download from here: | For this tutorials purpose we are using the Molecular Dynamics Code [https://manual.gromacs.org/documentation/ GROMACS] as this is a common simulation program and readily available on most clusters. We prepared three test systems with increasing amounts of water molecules which you can download from here: | ||
Revision as of 17:41, 20 September 2021
| Tutorial | |
|---|---|
| Title: | Benchmarking & Scaling |
| Provider: | HPC.NRW
|
| Contact: | tutorials@hpc.nrw |
| Type: | Online |
| Topic Area: | Performance Analysis |
| License: | CC-BY-SA |
| Syllabus
| |
| 1. Introduction & Theory | |
| 2. Interactive Manual Benchmarking | |
| 3. Automated Benchmarking using a Job Script | |
| 4. Automated Benchmarking using JUBE | |
| 5. Plotting & Interpreting Results | |
Prepare your input
It is always a good idea to create some test input for your simulation. If you have a specific system you want to benchmark for a production run make sure you limit the time the simulation is run for. If you also want to test some code given different input sizes of data, prepare those systems (or data-sets) beforehand.
For this tutorials purpose we are using the Molecular Dynamics Code GROMACS as this is a common simulation program and readily available on most clusters. We prepared three test systems with increasing amounts of water molecules which you can download from here:
- Download test input (tgz archive)
- SHA256 checksum:
d1677e755bf5feac025db6f427a929cbb2b881ee4b6e2ed13bda2b3c9a5dc8b0
The unpacked tar archive contains a folder with three binary input files (.tpr), which can directly be used as an input file for GROMACS. Those input files should be compatible with all GROMACS versions equal to or later than 2016.5:
| System | Sidelength of simulation box | No. of atoms |
|---|---|---|
| MD_5NM_WATER.tpr | 5nm | 12165 |
| MD_10NM_WATER.tpr | 10nm | 98319 |
| MD_15NM_WATER.tpr | 15nm | 325995 |
Allocate an interactive session
As a first measure you should allocate a single node on your cluster and start an interactive session, i.e. login on the node. Often there are dedicated partitions/queues named "express" or "testing" or the like, for exactly this purpose with a time limit of a few hours. For a cluster running SLURM this could for example look like:
srun -p express -N 1 -n 72 -t 02:00:00 --pty bash
This will allocate 1 node with 72 tasks on the express partition for 2 hours and log you in (i.e. start a new bash shell) on the allocated node. Adjust this according to your clusters provided resources!
Next: Automated Benchmarking using a Job Script
Previous: Introduction and Theory